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1.
Influenza Other Respir Viruses ; 17(5): e13150, 2023 05.
Article in English | MEDLINE | ID: covidwho-20236565

ABSTRACT

There are concerns that sotrovimab has reduced efficacy at reducing hospitalisation risk against the BA.2 sub-lineage of the Omicron SARS-CoV-2 variant. We performed a retrospective cohort (n = 8850) study of individuals treated with sotrovimab in the community, with the objective of assessing whether there were any differences in risk of hospitalisation of BA.2 cases compared with BA.1. We estimated that the hazard ratio of hospital admission with a length of stay of 2 days or more was 1.17 for BA.2 compared with BA.1 (95%CI 0.74-1.86). These results suggest that the risk of hospital admission was similar between the two sub-lineages.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Retrospective Studies , COVID-19/epidemiology , England/epidemiology
2.
Nat Commun ; 14(1): 3334, 2023 06 07.
Article in English | MEDLINE | ID: covidwho-20241659

ABSTRACT

COVID-19 patients at risk of severe disease may be treated with neutralising monoclonal antibodies (mAbs). To minimise virus escape from neutralisation these are administered as combinations e.g. casirivimab+imdevimab or, for antibodies targeting relatively conserved regions, individually e.g. sotrovimab. Unprecedented genomic surveillance of SARS-CoV-2 in the UK has enabled a genome-first approach to detect emerging drug resistance in Delta and Omicron cases treated with casirivimab+imdevimab and sotrovimab respectively. Mutations occur within the antibody epitopes and for casirivimab+imdevimab multiple mutations are present on contiguous raw reads, simultaneously affecting both components. Using surface plasmon resonance and pseudoviral neutralisation assays we demonstrate these mutations reduce or completely abrogate antibody affinity and neutralising activity, suggesting they are driven by immune evasion. In addition, we show that some mutations also reduce the neutralising activity of vaccine-induced serum.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , Antibodies, Monoclonal/therapeutic use , Immunotherapy , Mutation , Antibodies, Neutralizing , Antibodies, Viral
3.
Infect Prev Pract ; 5(2): 100281, 2023 Jun.
Article in English | MEDLINE | ID: covidwho-2307514

ABSTRACT

Introduction: Acquired carbapenemase-producing Gram-negative bacteria are an increasing public health concern globally and have been mandatory to report in England since October 2020. However, in light of the COVID-19 (SARS-CoV-2) pandemic, the Royal College of Pathologists (RCPath) released new guidance "for reducing the need for screening of CRE (carbapenem-resistant Enterobacterales) […] in low-risk areas", without defining "low risk". Methods: To assess the impact of the RCPath recommendations on screening of carbapenemase-producing Enterobacterales (CPE), an online Select Survey was sent to all NHS acute hospitals in England. The initial survey distribution was between March and April 2021 and the survey was relaunched between November 2021 and March 2022. Results: In total, 54 hospitals completed the survey, representing 39.1% of 138 eligible Trusts. All hospitals had a CPE screening policy in place, and the majority of these reflect UKHSA's Framework of actions to contain CPE. Of the 23 hospitals who reported a reduction in CPE screening, only three (13.0%) indicated that this was due to the RCPath recommendations, with 21 (91.3%) indicating that there had been a natural reduction in the number of patients admitted to the Trust who would have previously been screened due to the COVID-19 pandemic. Conclusion: For most surveyed hospitals, CPE screening was not reduced due to the RCPath recommendations. However, the results highlighted that there is a large amount of individual variation in CPE screening practices and diagnostic testing between hospitals.

5.
Emerg Infect Dis ; 29(1)2022 Dec 01.
Article in English | MEDLINE | ID: covidwho-2230070

ABSTRACT

Since June 2020, the SARS-CoV-2 Immunity and Reinfection Evaluation (SIREN) study has conducted routine PCR testing in UK healthcare workers and sequenced PCR-positive samples. SIREN detected increases in infections and reinfections during Omicron subvariant waves contemporaneous with national surveillance. SIREN's sentinel surveillance methods can be used for variant surveillance.

6.
Bone Joint J ; 104-B(10): 1156-1167, 2022 Oct.
Article in English | MEDLINE | ID: covidwho-2196752

ABSTRACT

AIMS: Hip fracture commonly affects the frailest patients, of whom many are care-dependent, with a disproportionate risk of contracting COVID-19. We examined the impact of COVID-19 infection on hip fracture mortality in England. METHODS: We conducted a cohort study of patients with hip fracture recorded in the National Hip Fracture Database between 1 February 2019 and 31 October 2020 in England. Data were linked to Hospital Episode Statistics to quantify patient characteristics and comorbidities, Office for National Statistics mortality data, and Public Health England's SARS-CoV-2 testing results. Multivariable Cox regression examined determinants of 90-day mortality. Excess mortality attributable to COVID-19 was quantified using Quasi-Poisson models. RESULTS: Analysis of 102,900 hip fractures (42,630 occurring during the pandemic) revealed that among those with COVID-19 infection at presentation (n = 1,120) there was a doubling of 90-day mortality; hazard ratio (HR) 2.09 (95% confidence interval (CI) 1.89 to 2.31), while the HR for infections arising between eight and 30 days after presentation (n = 1,644) the figure was greater at 2.51 (95% CI 2.31 to 2.73). Malnutrition (1.45 (95% CI 1.19 to 1.77)) and nonoperative treatment (2.94 (95% CI 2.18 to 3.95)) were the only modifiable risk factors for death in COVID-19-positive patients. Patients who had tested positive for COVID-19 more than two weeks prior to hip fracture initially had better survival compared to those who contracted COVID-19 around the time of their hip fracture; however, survival rapidly declined and by 365 days the combination of hip fracture and COVID-19 infection was associated with a 50% mortality rate. Between 1 January and 30 June 2020, 1,273 (99.7% CI 1,077 to 1,465) excess deaths occurred within 90 days of hip fracture, representing an excess mortality of 23% (99.7% CI 20% to 26%), with most deaths occurring within 30 days. CONCLUSION: COVID-19 infection more than doubles the rate of early hip fracture mortality. Those contracting infection between 8 and 30 days after initial presentation are at even higher mortality risk, signalling the potential for targeted interventions during this period to improve survival.Cite this article: Bone Joint J 2022;104-B(10):1156-1167.


Subject(s)
COVID-19 , Hip Fractures , COVID-19/complications , COVID-19 Testing , Cohort Studies , England/epidemiology , Hip Fractures/surgery , Humans , SARS-CoV-2
7.
BMJ Open ; 12(9): e060992, 2022 09 01.
Article in English | MEDLINE | ID: covidwho-2009221

ABSTRACT

OBJECTIVES: Across diverse ethnic groups in the UK, explore attitudes and intentions towards COVID-19 vaccination and sources of COVID-19 information. DESIGN: Remote qualitative interviews and focus groups (FGs) conducted June-October 2020 before UK COVID-19 vaccine approval. Data were transcribed and analysed through inductive thematic analysis and mapped to the Theoretical Domains Framework. SETTING: England and Wales. PARTICIPANTS: 100 participants from 19 self-identified ethnic groups. RESULTS: Mistrust and doubt were reported across ethnic groups. Many participants shared concerns about perceived lack of information about COVID-19 vaccine safety and efficacy. There were differences within each ethnic group, with factors such as occupation and perceived health status influencing intention to accept a vaccine once made available. Across ethnic groups, participants believed that public contact occupations, older adults and vulnerable groups should be prioritised for vaccination. Perceived risk, social influences, occupation, age, comorbidities and engagement with healthcare influenced participants' intentions to accept vaccination once available. All Jewish FG participants intended to accept, while all Traveller FG participants indicated they probably would not.Facilitators to COVID-19 vaccine uptake across ethnic groups included: desire to return to normality and protect health and well-being; perceived higher risk of infection; evidence of vaccine safety and efficacy; vaccine availability and accessibility.COVID-19 information sources were influenced by social factors and included: friends and family; media and news outlets; research literature; and culture and religion. Participants across most different ethnic groups were concerned about misinformation or had negative attitudes towards the media. CONCLUSIONS: During vaccination rollout, including boosters, commissioners and providers should provide accurate information, authentic community outreach and use appropriate channels to disseminate information and counter misinformation. Adopting a context-specific approach to vaccine resources, interventions and policies and empowering communities has potential to increase trust in the programme.


Subject(s)
COVID-19 , Vaccines , Humans , Aged , COVID-19/prevention & control , COVID-19 Vaccines , Ethnicity , Information Sources , Vaccination , England , Attitude
8.
J Infect ; 85(5): 545-556, 2022 11.
Article in English | MEDLINE | ID: covidwho-2007862

ABSTRACT

OBJECTIVES: To investigate serological differences between SARS-CoV-2 reinfection cases and contemporary controls, to identify antibody correlates of protection against reinfection. METHODS: We performed a case-control study, comparing reinfection cases with singly infected individuals pre-vaccination, matched by gender, age, region and timing of first infection. Serum samples were tested for anti-SARS-CoV-2 spike (anti-S), anti-SARS-CoV-2 nucleocapsid (anti-N), live virus microneutralisation (LV-N) and pseudovirus microneutralisation (PV-N). Results were analysed using fixed effect linear regression and fitted into conditional logistic regression models. RESULTS: We identified 23 cases and 92 controls. First infections occurred before November 2020; reinfections occurred before February 2021, pre-vaccination. Anti-S levels, LV-N and PV-N titres were significantly lower among cases; no difference was found for anti-N levels. Increasing anti-S levels were associated with reduced risk of reinfection (OR 0·63, CI 0·47-0·85), but no association for anti-N levels (OR 0·88, CI 0·73-1·05). Titres >40 were correlated with protection against reinfection for LV-N Wuhan (OR 0·02, CI 0·001-0·31) and LV-N Alpha (OR 0·07, CI 0·009-0·62). For PV-N, titres >100 were associated with protection against Wuhan (OR 0·14, CI 0·03-0·64) and Alpha (0·06, CI 0·008-0·40). CONCLUSIONS: Before vaccination, protection against SARS-CoV-2 reinfection was directly correlated with anti-S levels, PV-N and LV-N titres, but not with anti-N levels. Detectable LV-N titres were sufficient for protection, whilst PV-N titres >100 were required for a protective effect. TRIAL REGISTRATION NUMBER: ISRCTN11041050.


Subject(s)
COVID-19 , SARS-CoV-2 , Antibodies, Viral , COVID-19/prevention & control , Case-Control Studies , Humans , Reinfection/prevention & control , Vaccination
9.
BMJ Open ; 12(8): e061027, 2022 08 17.
Article in English | MEDLINE | ID: covidwho-1993022

ABSTRACT

OBJECTIVES: To explore public reactions to the COVID-19 pandemic across diverse ethnic groups. DESIGN: Remote qualitative interviews and focus groups in English or Punjabi. Data were transcribed and analysed through inductive thematic analysis. SETTING: England and Wales, June to October 2020. PARTICIPANTS: 100 participants from 19 diverse 'self-identified' ethnic groups. RESULTS: Dismay, frustration and altruism were reported across all ethnic groups during the first 6-9 months of the COVID-19 pandemic. Dismay was caused by participants' reported individual, family and community risks, and loss of support networks. Frustration was caused by reported lack of recognition of the efforts of ethnic minority groups (EMGs), inaction by government to address COVID-19 and inequalities, rule breaking by government advisors, changing government rules around: border controls, personal protective equipment, social distancing, eating out, and perceived poor communication around COVID-19 and the Public Health England COVID-19 disparities report (leading to reported increased racism and social isolation). Altruism was felt by all, in the resilience of National Health Service (NHS) staff and their communities and families pulling together. Data, participants' suggested actions and the behaviour change wheel informed suggested interventions and policies to help control COVID-19. CONCLUSION: To improve trust and compliance future reports or guidance should clearly explain any stated differences in health outcomes by ethnicity or other risk group, including specific messages for these groups and concrete actions to minimise any risks. Messaging should reflect the uncertainty in data or advice and how guidance may change going forward as new evidence becomes available. A contingency plan is needed to mitigate the impact of COVID-19 across all communities including EMGs, the vulnerable and socially disadvantaged individuals, in preparation for any rise in cases and for future pandemics. Equality across ethnicities for healthcare is essential, and the NHS and local communities will need to be supported to attain this.


Subject(s)
COVID-19 , COVID-19/epidemiology , Ethnicity , Humans , Minority Groups , Pandemics , State Medicine
10.
BMC Infect Dis ; 22(1): 556, 2022 Jun 18.
Article in English | MEDLINE | ID: covidwho-1962756

ABSTRACT

BACKGROUND: SARS-CoV-2 is known to transmit in hospital settings, but the contribution of infections acquired in hospitals to the epidemic at a national scale is unknown. METHODS: We used comprehensive national English datasets to determine the number of COVID-19 patients with identified hospital-acquired infections (with symptom onset > 7 days after admission and before discharge) in acute English hospitals up to August 2020. As patients may leave the hospital prior to detection of infection or have rapid symptom onset, we combined measures of the length of stay and the incubation period distribution to estimate how many hospital-acquired infections may have been missed. We used simulations to estimate the total number (identified and unidentified) of symptomatic hospital-acquired infections, as well as infections due to onward community transmission from missed hospital-acquired infections, to 31st July 2020. RESULTS: In our dataset of hospitalised COVID-19 patients in acute English hospitals with a recorded symptom onset date (n = 65,028), 7% were classified as hospital-acquired. We estimated that only 30% (range across weeks and 200 simulations: 20-41%) of symptomatic hospital-acquired infections would be identified, with up to 15% (mean, 95% range over 200 simulations: 14.1-15.8%) of cases currently classified as community-acquired COVID-19 potentially linked to hospital transmission. We estimated that 26,600 (25,900 to 27,700) individuals acquired a symptomatic SARS-CoV-2 infection in an acute Trust in England before 31st July 2020, resulting in 15,900 (15,200-16,400) or 20.1% (19.2-20.7%) of all identified hospitalised COVID-19 cases. CONCLUSIONS: Transmission of SARS-CoV-2 to hospitalised patients likely caused approximately a fifth of identified cases of hospitalised COVID-19 in the "first wave" in England, but less than 1% of all infections in England. Using time to symptom onset from admission for inpatients as a detection method likely misses a substantial proportion (> 60%) of hospital-acquired infections.


Subject(s)
COVID-19 , Cross Infection , COVID-19/epidemiology , Cross Infection/epidemiology , Hospitalization , Hospitals , Humans , SARS-CoV-2
11.
BMJ ; 378: e070379, 2022 07 20.
Article in English | MEDLINE | ID: covidwho-1950079

ABSTRACT

OBJECTIVE: To describe the incidence of, risk factors for, and impact of vaccines on primary SARS-CoV-2 infection during the second wave of the covid-19 pandemic in susceptible hospital healthcare workers in England. DESIGN: Multicentre prospective cohort study. SETTING: National Health Service secondary care health organisations (trusts) in England between 1 September 2020 and 30 April 2021. PARTICIPANTS: Clinical, support, and administrative staff enrolled in the SARS-CoV-2 Immunity and Reinfection Evaluation (SIREN) study with no evidence of previous infection. Vaccination status was obtained from national covid-19 vaccination registries and self-reported. MAIN OUTCOME MEASURE: SARS-CoV-2 infection confirmed by polymerase chain reaction. Mixed effects logistic regression was conducted to determine demographic and occupational risk factors for infection, and an individual based mathematical model was used to predict how large the burden could have been if vaccines had not been available from 8 December 2020 . RESULTS: During England's second wave, 12.9% (2353/18 284) of susceptible SIREN participants became infected with SARS-CoV-2. Infections peaked in late December 2020 and decreased from January 2021, concurrent with the cohort's rapid vaccination coverage and a national lockdown. In multivariable analysis, factors increasing the likelihood of infection in the second wave were being under 25 years old (20.3% (132/651); adjusted odds ratio 1.35, 95% confidence interval 1.07 to 1.69), living in a large household (15.8% (282/1781); 1.54, 1.23 to 1.94, for participants from households of five or more people), having frequent exposure to patients with covid-19 (19.2% (723/3762); 1.79, 1.56 to 2.06, for participants with exposure every shift), working in an emergency department or inpatient ward setting (20.8% (386/1855); 1.76, 1.45 to 2.14), and being a healthcare assistant (18.1% (267/1479); 1.43, 1.16 to 1.77). Time to first vaccination emerged as being strongly associated with infection (P<0.001), with each additional day multiplying a participant's adjusted odds ratio by 1.02. Mathematical model simulations indicated that an additional 9.9% of all patient facing hospital healthcare workers would have been infected were it not for the rapid vaccination coverage. CONCLUSIONS: The rapid covid-19 vaccine rollout from December 2020 averted infection in a large proportion of hospital healthcare workers in England: without vaccines, second wave infections could have been 69% higher. With booster vaccinations being needed for adequate protection from the omicron variant, and perhaps the need for further boosters for future variants, ensuring equitable delivery to healthcare workers is essential. The findings also highlight occupational risk factors that persisted in healthcare workers despite vaccine rollout; a greater understanding of the transmission dynamics responsible for these is needed to help to optimise the infection prevention and control policies that protect healthcare workers from infection and therefore to support staffing levels and maintain healthcare provision. TRIAL REGISTRATION: ISRCTN registry ISRCTN11041050.


Subject(s)
COVID-19 , Vaccines , Adult , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19 Vaccines , Communicable Disease Control , Health Personnel , Humans , Models, Theoretical , Pandemics/prevention & control , Prospective Studies , SARS-CoV-2 , State Medicine
12.
BMJ Open ; 12(6): e054336, 2022 06 28.
Article in English | MEDLINE | ID: covidwho-1909750

ABSTRACT

INTRODUCTION: Understanding the effectiveness and durability of protection against SARS-CoV-2 infection conferred by previous infection and COVID-19 is essential to inform ongoing management of the pandemic. This study aims to determine whether prior SARS-CoV-2 infection or COVID-19 vaccination in healthcare workers protects against future infection. METHODS AND ANALYSIS: This is a prospective cohort study design in staff members working in hospitals in the UK. At enrolment, participants are allocated into cohorts, positive or naïve, dependent on their prior SARS-CoV-2 infection status, as measured by standardised SARS-CoV-2 antibody testing on all baseline serum samples and previous SARS-CoV-2 test results. Participants undergo monthly antibody testing and fortnightly viral RNA testing during follow-up and based on these results may move between cohorts. Any results from testing undertaken for other reasons (eg, symptoms, contact tracing) or prior to study entry will also be captured. Individuals complete enrolment and fortnightly questionnaires on exposures, symptoms and vaccination. Follow-up is 12 months from study entry, with an option to extend follow-up to 24 months.The primary outcome of interest is infection with SARS-CoV-2 after previous SARS-CoV-2 infection or COVID-19 vaccination during the study period. Secondary outcomes include incidence and prevalence (both RNA and antibody) of SARS-CoV-2, viral genomics, viral culture, symptom history and antibody/neutralising antibody titres. ETHICS AND DISSEMINATION: The study was approved by the Berkshire Research Ethics Committee, Health Research Authority (IRAS ID 284460, REC reference 20/SC/0230) on 22 May 2020; the vaccine amendment was approved on 12 January 2021. Participants gave informed consent before taking part in the study.Regular reports to national and international expert advisory groups and peer-reviewed publications ensure timely dissemination of findings to inform decision making. TRIAL REGISTRATION NUMBER: ISRCTN11041050.


Subject(s)
COVID-19 , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19 Vaccines , Health Personnel , Humans , Incidence , Multicenter Studies as Topic , Prospective Studies , RNA, Viral , Reinfection , SARS-CoV-2 , United Kingdom/epidemiology , Vaccination
13.
N Engl J Med ; 386(13): 1207-1220, 2022 03 31.
Article in English | MEDLINE | ID: covidwho-1692473

ABSTRACT

BACKGROUND: The duration and effectiveness of immunity from infection with and vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are relevant to pandemic policy interventions, including the timing of vaccine boosters. METHODS: We investigated the duration and effectiveness of immunity in a prospective cohort of asymptomatic health care workers in the United Kingdom who underwent routine polymerase-chain-reaction (PCR) testing. Vaccine effectiveness (≤10 months after the first dose of vaccine) and infection-acquired immunity were assessed by comparing the time to PCR-confirmed infection in vaccinated persons with that in unvaccinated persons, stratified according to previous infection status. We used a Cox regression model with adjustment for previous SARS-CoV-2 infection status, vaccine type and dosing interval, demographic characteristics, and workplace exposure to SARS-CoV-2. RESULTS: Of 35,768 participants, 27% (9488) had a previous SARS-CoV-2 infection. Vaccine coverage was high: 95% of the participants had received two doses (78% had received BNT162b2 vaccine [Pfizer-BioNTech] with a long interval between doses, 9% BNT162b2 vaccine with a short interval between doses, and 8% ChAdOx1 nCoV-19 vaccine [AstraZeneca]). Between December 7, 2020, and September 21, 2021, a total of 2747 primary infections and 210 reinfections were observed. Among previously uninfected participants who received long-interval BNT162b2 vaccine, adjusted vaccine effectiveness decreased from 85% (95% confidence interval [CI], 72 to 92) 14 to 73 days after the second dose to 51% (95% CI, 22 to 69) at a median of 201 days (interquartile range, 197 to 205) after the second dose; this effectiveness did not differ significantly between the long-interval and short-interval BNT162b2 vaccine recipients. At 14 to 73 days after the second dose, adjusted vaccine effectiveness among ChAdOx1 nCoV-19 vaccine recipients was 58% (95% CI, 23 to 77) - considerably lower than that among BNT162b2 vaccine recipients. Infection-acquired immunity waned after 1 year in unvaccinated participants but remained consistently higher than 90% in those who were subsequently vaccinated, even in persons infected more than 18 months previously. CONCLUSIONS: Two doses of BNT162b2 vaccine were associated with high short-term protection against SARS-CoV-2 infection; this protection waned considerably after 6 months. Infection-acquired immunity boosted with vaccination remained high more than 1 year after infection. (Funded by the U.K. Health Security Agency and others; ISRCTN Registry number, ISRCTN11041050.).


Subject(s)
Adaptive Immunity , COVID-19 Vaccines , COVID-19 , SARS-CoV-2 , Adaptive Immunity/immunology , Asymptomatic Diseases , BNT162 Vaccine/therapeutic use , COVID-19/diagnosis , COVID-19/immunology , COVID-19/prevention & control , COVID-19 Nucleic Acid Testing , COVID-19 Vaccines/immunology , COVID-19 Vaccines/therapeutic use , ChAdOx1 nCoV-19/therapeutic use , Health Personnel , Humans , Prospective Studies , United Kingdom , Vaccination/methods , Vaccine Efficacy
14.
BMJ ; 376: o35, 2022 01 17.
Article in English | MEDLINE | ID: covidwho-1627545
16.
J Antimicrob Chemother ; 77(3): 799-802, 2022 02 23.
Article in English | MEDLINE | ID: covidwho-1569708

ABSTRACT

BACKGROUND: Antibacterial prescribing for respiratory tract infections (RTIs) accounts for almost half of all prescribing in primary care. Nearly a quarter of antibacterial prescribing in primary care is estimated to be inappropriate, the greatest being for RTIs. The COVID-19 pandemic has changed the provision of healthcare services and impacted the levels of antibacterials prescribed. OBJECTIVES: To describe the changes in community antibacterial prescribing for RTIs in winter 2020-21 in England. METHODS: RTI antibacterial prescribing was measured in prescription items/1000 population for primary care from January 2014 and in DDDs/1000 population/day for the totality of RTI prescribing [combined with Accident & Emergency (A&E) in secondary care], from January 2016 to February 2021. Trends were assessed using negative binomial regression and seasonally adjusted interrupted time-series analysis. RESULTS: Antibacterials prescribed for RTIs reduced by a further 12.4% per season compared with pre-COVID (P < 0.001). In winter 2020-21, RTI prescriptions almost halved compared with the previous winter in 2019-20 (P < 0.001). The trend observed for total RTI prescribing (primary care with A&E) was similar to that observed in the community alone. CONCLUSIONS: During COVID-19, RTI prescribing reduced in the community and the expected rise in winter was not seen in 2020-21. We found no evidence that RTI prescribing shifted from primary care to A&E in secondary care. The most likely explanation is a decrease in RTIs and presentations to primary care associated with national prevention measures for COVID-19.


Subject(s)
COVID-19 , Respiratory Tract Infections , Anti-Bacterial Agents/therapeutic use , England/epidemiology , Humans , Inappropriate Prescribing/prevention & control , Pandemics , Practice Patterns, Physicians' , Primary Health Care , Respiratory Tract Infections/drug therapy , Respiratory Tract Infections/epidemiology , SARS-CoV-2 , Seasons
18.
Int J STD AIDS ; 33(2): 209-211, 2022 02.
Article in English | MEDLINE | ID: covidwho-1542033

ABSTRACT

We describe the case of a 30-year-old care home employee diagnosed with COVID-19 and acute untreated HIV-1. He was unable to return to work for 119 days due to concerns over transmission risk as his SARS-CoV-2 PCR remained detectable. This highlights the uncertainty in interpreting SARS-CoV-2 PCR results post-infection in acute untreated HIV.


Subject(s)
COVID-19 , HIV Infections , HIV-1 , Adult , HIV Infections/complications , HIV Infections/drug therapy , Humans , Male , Return to Work , SARS-CoV-2
19.
Lancet Microbe ; 3(2): e151-e158, 2022 02.
Article in English | MEDLINE | ID: covidwho-1440435

ABSTRACT

We reviewed all genomic epidemiology studies on COVID-19 in long-term care facilities (LTCFs) that had been published to date. We found that staff and residents were usually infected with identical, or near identical, SARS-CoV-2 genomes. Outbreaks usually involved one predominant cluster, and the same lineages persisted in LTCFs despite infection control measures. Outbreaks were most commonly due to single or few introductions followed by a spread rather than a series of seeding events from the community into LTCFs. The sequencing of samples taken consecutively from the same individuals at the same facilities showed the persistence of the same genome sequence, indicating that the sequencing technique was robust over time. When combined with local epidemiology, genomics allowed probable transmission sources to be better characterised. The transmission between LTCFs was detected in multiple studies. The mortality rate among residents was high in all facilities, regardless of the lineage. Bioinformatics methods were inadequate in a third of the studies reviewed, and reproducing the analyses was difficult because sequencing data were not available in many facilities.


Subject(s)
COVID-19 , COVID-19/epidemiology , Disease Outbreaks , Genomics , Humans , Long-Term Care , SARS-CoV-2/genetics
20.
Clin Microbiol Infect ; 27(11): 1658-1665, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1392218

ABSTRACT

OBJECTIVES: The impact of bacterial/fungal infections on the morbidity and mortality of persons with coronavirus disease 2019 (COVID-19) remains unclear. We have investigated the incidence and impact of key bacterial/fungal infections in persons with COVID-19 in England. METHODS: We extracted laboratory-confirmed cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (1st January 2020 to 2nd June 2020) and blood and lower-respiratory specimens positive for 24 genera/species of clinical relevance (1st January 2020 to 30th June 2020) from Public Health England's national laboratory surveillance system. We defined coinfection and secondary infection as a culture-positive key organism isolated within 1 day or 2-27 days, respectively, of the SARS-CoV-2-positive date. We described the incidence and timing of bacterial/fungal infections and compared characteristics of COVID-19 patients with and without bacterial/fungal infection. RESULTS: 1% of persons with COVID-19 (2279/223413) in England had coinfection/secondary infection, of which >65% were bloodstream infections. The most common causative organisms were Escherichia coli, Staphylococcus aureus and Klebsiella pneumoniae. Cases with coinfection/secondary infections were older than those without (median 70 years (IQR 58-81) versus 55 years (IQR 38-77)), and a higher percentage of cases with secondary infection were of Black or Asian ethnicity than cases without (6.7% versus 4.1%, and 9.9% versus 8.2%, respectively, p < 0.001). Age-sex-adjusted case fatality rates were higher in COVID-19 cases with a coinfection (23.0% (95%CI 18.8-27.6%)) or secondary infection (26.5% (95%CI 14.5-39.4%)) than in those without (7.6% (95%CI 7.5-7.7%)) (p < 0.005). CONCLUSIONS: Coinfection/secondary bacterial/fungal infections were rare in non-hospitalized and hospitalized persons with COVID-19, varied by ethnicity and age, and were associated with higher mortality. However, the inclusion of non-hospitalized persons with asymptomatic/mild COVID-19 likely underestimated the rate of secondary bacterial/fungal infections. This should inform diagnostic testing and antibiotic prescribing strategy.


Subject(s)
Bacterial Infections , COVID-19 , Coinfection , Mycoses , Adult , Aged , Bacterial Infections/epidemiology , COVID-19/epidemiology , Coinfection/epidemiology , England/epidemiology , Humans , Middle Aged , Mycoses/epidemiology
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